Category Archives: Ricerca

New dataset on bacterial and fungal communities of table olives.

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A new dataset with a collection of published metataxonomic studies on bacterial communities of table olives has just been released. You can find it here:

https://github.com/ep142/Metaolive

You can use it with your own data and obtain quantitative comparisons of microbial communities of table olives and their environments in published studies. All new data produced in our METAolive project will end up here. The dataset is extracted from FoodMicrobionet v5.

If you want to see a use case checkout our poster presented at the Food Systems Microbiomes meeting, held in Turin from 14/5 to 17/5.

This project is co-funded by Ministero dell’Università e della Ricerca PRIN 2022, proposal 2022NN28ZZ, and received funding from the European Union Next-GenerationEU – PIANO NAZIONALE DI RIPRESA E RESILIENZA (PNRR).

FoodMicrobionet 5 is now available!

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The new major version includes (finally) fungi. As usual, you can find everything you need:

This version is currently co-funded by Ministero dell’Università e della Ricerca PRIN 2022 PNRR, proposal P20229JMMH, Mining the biodiversity of non conventional yeasts as bioresources for innovative fermented beverages through a genomics, and received funding from the European Union Next-GenerationEU (PIANO NAZIONALE DI RIPRESA E RESILIENZA (PNRR)) CUP C53D23007560001

We are recruiting!

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There is a position open for a junior PostDoc (i.e. no experience required except a PhD in a suitable disciplinary area). International candidates are welcome as long as they are fluent in English and are able to speak some Italian. The PostDoc will work on the METAOLIVE project and is expected to co-ordinate the activity of MSc students during their Research thesis. The duration of the contract is 12 months and the gross salary 25 k€. Applications for the selection process closes on January 20th.

If you want to learn more:

International candidates are encouraged to contact me (Eugenio Parente, I am pretty sure you can find the e-mail address) before submitting an application.

FoodMicrobionet 4.2.1 is now available

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I have just released a new version of FoodMicrobionet. Version 4.2.1 includes 233 studies and 13895 food and food environment samples. New tables have been added (Abstracts table) and metadata for studies (a study_type field now provides a classification in longitudinal cross-sectional or mixed for the study design) have been improved. You can access the new version:

  • on GitHub: data in the the_real_thing folder, plus a bunch of scripts
  • on Zenodo: here you can find the mindata files, with ASV sequences
  • on Mendeley data (the most recent version is in moderation, reserved DOI 10.17632/8fwwjpm79y.8)

Share (using the DOIs provided by Mendeley data and Zenodo) and enjoy. You can find the most recent publications on FMBN here.

New Foodmicrobionet publication

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Our last publication obtained using data in FoodMicrobionet is:
Parente, E., Zotta, T., Giavalisco, M., Ricciardi, A., 2023. Metataxonomic insights in the distribution of Lactobacillaceae in foods and food environments. Int J Food Microbiol 110124. https://doi.org/10.1016/j.ijfoodmicro.2023.110124
The code is pretty general and the work can be easily replicated for any other microbial group in FoodMicrobionet.
You can download a free .pdf (until 5/4/2023) here https://authors.elsevier.com/a/1gerCcF3iFHfL

Literature cited, project 2017J2RMTN

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  1. Berni Canani, , De Filippis, F., et al. 2017. Appl. Environ. Microbiol. 83: e01206-17.  https://dx.doi.org/10.1128/AEM.01206-17.
  2. Bokulich, N. A., Mills, D.A. 2013. Appl. Environmen. Microbiol. 79: 2519–226.  https://dx.doi.org/10.1128/AEM.03870-12.
  3. Callahan, B. J., McMurdie, P. J., Holmes, S. P.. 2017. ISME J. 11: 2639–4263. https://dx.doi.org/10.1038/ismej.2017.119.
  4. Callahan, B. J., McMurdie, P. J., Rosen, M. J., Han, A. W., Johnson, A.J.A., Holmes, S. P. 2016. Nature Meth. 13: 581–583. https://dx.doi.org/10.1038/nmeth.3869.
  5. De Filippis, F., Parente, E., Ercolini, D. 2017a. Microbial Biotechnol. 10: 91–102. https://dx.doi.org/10.1111/1751-7915.12421.
  6. De Filippis, F., Laiola, M., Blaiotta, G., Ercolini, D.. 2017b. Appl. Environ. Microbiol., 83: e00905–17. https://dx.doi.org/10.1128/AEM.00905-17.
  7. De Filippis, F., Parente, E., Danilo Ercolini. Ann. Rev. Food Sci. Technol. 9. https://dx.doi.org/10.1146/annurev-food-030117-012312.
  8. De Filippis, F., Parente, E., Zotta, T., Ercolini, D. 2018b. J. Food Microbiol. 265: 9–17. https://dx.doi.org/10.1016/j.ijfoodmicro.2017.10.028.
  9. EFSA (2015). The food classification and description system FoodEx 2 (revision 2). Supporting publication 2015:EN-804. http://www.efsa.europa.eu/en/supporting/pub/215e.htm
  10. Emerson, J. B., Adams, R. I., Betancourt Román C. M., Brooks, B., Coil, D. A., Dahlhausen, Holly H. Ganz, K., et al. 2017. Microbiome 5: 86. https://dx.doi.org/10.1186/s40168-017-0285-3.
  11. Erkus, O., de Jager, V.C.L., Geene, R. T. C. M., van Alen-Boerrigter, I., Hazelwood, L., van Hijum, S. A .F. T., Kleerebezem, M., Smid, E. J. 2016. Int. J. Food Microbiol. 228: 1–9. https://dx.doi.org/10.1016/j.ijfoodmicro.2016.03.027.
  12. Faust, K., Raes, J. 2016. F1000Research 5: 1519–14. https://dx.doi.org/10.12688/f1000research.9050.2.
  13. Fouhy, F., Clooney, A. G., Stanton, C., Claesson, M.J., Cotter, P. D. 2016. BMC Microbiol. 16: 123. https://dx.doi.org/10.1186/s12866-016-0738-z.
  14. Garofalo, C., Osimani, A., Milanovic, V., Aquilanti, L., De Filippis, F., Stellato, G., Di Mauro, S., Turchetti, B., Buzzini, P., Ercolini, D., Clementi, F., 2015. Food Microbiol. 49: 123-133. https://dx.doi.org/10.1016/j.fm.2015.01.017
  15. Humblot, C., Guyot, J.-P. 2009. Appl. Environ. Microbiol. 75: 4354–4361. https://dx.doi.org/10.1128/AEM.00451-09.
  16. Kuuliala, L., Al Hage, Y., Ioannidis, A.-G., Sader, M., Kerckhof, F.-M., Vanderroost, M., Boon, N. et al. 2018. Food Microbiol. 70: 232–44. https://dx.doi.org/10.1016/j.fm.2017.10.011.
  17. Layeghifard, M., Hwang, D. M., Guttman, D. S. 2017. Trends Microbiol. 25: 217–28. https://dx.doi.org/10.1016/j.tim.2016.11.008.
  18. Levy, S.E., Myers, R.M. 2016. Annu. Rev. Genom. Hum. Genet. 17:95-115. https://dx.doi.org/10.1146/annurev-genom-083115-022413
  19. McDonald, D., Price, M.N., Goodrich, J., et al. 2012. ISME J. 6(3): 610-618. https://dx.doi.org/1038/ismej.2011.139.
  20. McMurdie, P. J., Susan Holmes. 2015. Bioinformatics 31: 282–283. https://dx.doi.org/10.1093/bioinformatics/btu616.
  21. Mitchell, A. L., Scheremetjew, M., Denise, H., Potte, S., Tarkowska, A., Qureshi, M., Salazar, G. A., et al. 2018. Nucleic Acids Research 46: D726–35. https://dx.doi.org/10.1093/nar/gkx967.
  22. Nature Editorial 2016. Nature Microbiology 1: 16112. https://dx.doi.org/10.1038/nmicrobiol.2016.112
  23. Parente, E., Cocolin, L., De Filippis, F., Zotta, T., Ferrocino, I., O’Sullivan, O., Neviani, E., De Angelis, M., Cotter, P. D., Ercolini, D. 2016. Int. J. Food Microbiol. 219 28–37. https://dx.doi.org/10.1016/j.ijfoodmicro.2015.12.001.
  24. Parente, E., Zotta, T., Faust, K., De Filippis, F., Ercolini, D. 2018. Food Microbiol. 73: 49-60. https://dx.doi.org/10.1016/j.fm.2017.12.010.
  25. Quast, C., Pruesse, E., Yilmaz, P., Gerken, J., Schweer, T., Yarza, P. et al. 2013. Nucl. Ac. Res. 41 (Database issue): D590–96.  https://dx.doi.org/10.1093/nar/gks1219.
  26. Qin J, et al. 2010. Nature. 464: 59-65. https://dx.doi.org/10.1038/nature08821.
  27. Quince, C., Walker, A.W., Simpson, J.T., Loman, N.J., Segata, N. 2017. Nat. Biotechnol. 35: 833-844. https://dx.doi.org/10.1038/nbt.3935.
  28. Sedlar, K., Kupkova, K., Provaznik, I. 2017. Comput. Struct. Biotecnol. J. 15: 48-55.  https://dx.doi.org/1016/j.csbj.2016.11.005.
  29. Singer, Esther, Bill Andreopoulos, Robert M Bowers, Janey Lee, Shweta Deshpande, Jennifer Chiniquy, Doina Ciobanu, et al. 2016. Scientific Data 3: 160081. https://dx.doi.org/10.1038/sdata.2016.81.
  30. Stellato, G., De Filippis, F., La Storia, A., Ercolini, D. 2015. and Envirn. Microbiol. 81:7893-7904. https://dx.doi.org/10.1128/AEM.02294-15.
  31. Thompson, L. R, Sanders, J. G., McDonald, D., Amir, A., Ladau, J., Locey, K. J., Prill, R. J. et al. 2017. Nature 104: 457-465. https://dx.doi.org/10.1038/nature24621.
  32. Vandeputte, D., Tito, R.Y., Vanleeuwen, R., Falony, G., Raes, J. 2017. FEMS Microbiol. Rev. 41: S154–67. https://dx.doi.org/10.1093/femsre/fux027.
  33. Zhou, J., He, Z., Yang, Y., Deng, Y., Tringe, S. G., Alvarez-Cohen. L. 2015. mBio 6 (1). https://dx.doi.org/10.1128/mBio.02288-14.

MIND@FoodMicro2016

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We will be in Dublin for FoodMicro 2016. Here you can download .pdf versions of our posters. You can find more in the FoodMicrobionet website.

  • PO1-FB-075 DIVERSITY OF STREPTOCOCCUS THERMOPHILUS POPULATIONS BY PHOSPHOSERINE PHOSPHATASE (SER-B) POLYMORPHISMS Teresa Zotta*, Annamaria Ricciardi, Francesca De Filippis, Danilo Ercolini, Eugenio Parente
  • PO1-FB-074 PURIFICATION AND FUNCTIONAL CHARACTERIZATION OF HEME-DEPENDENT CATALASE IN RESPIRATIVE STRAIN LACTOBACILLUS CASEI N87 Teresa Zotta, Antonio Varriale, Rocco G. Ianniello, Eugenio Parente, Maria C. Staiano, Annamaria Ricciardi
  • PO1-FB-073 EFFECT OF RESPIRATIVE AND CATALASE-POSITIVE CULTURES OF LACTOBACILLUS CASEI ON THE PRODUCTION OF CHEDDAR CHEESE Annamaria Ricciardi, Anna Reale, Rocco G. Ianniello, Felicia Ciocia, Tiziana Di Renzo, Teresa Zotta, Floriana Boscaino, Raffaele Coppola, Eugenio Parente, Paul L. H. McSweeney